How best to clear out space on disk and avoid duplicates

That’s exactly right.  You broke the backup when you deleted the file from the backup folder.  Now, it’s not going to backup correctly.  You will need to redo the backup. 

What, Trancer was trying to tell you is that the software is a backup software, so it does NOT track what you change in your original directories, nor does it sync them up.  When you move things around, alot, you will end up with many copies.  However, you should still be able to see which is the most recent, based on the current location of the file.

If you’re going to be always moving files around and rearrange them, you will need to consider a sync program to help you out with that.

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